There is considerable discussion about the relative importance of conserving high quality wilderness areas (i.e. large and intact landscapes) versus conserving areas with high biodiversity values. Places that are needed to achieve one aspect of biodiversity conservation are not necessarily optimal for another which can lead to conflict in assigning conservation priorities. However, both are important for biodiversity conservation, and carry social, economic, and ecological values. Investment in both (a) representation of elements of biodiversity (e.g. species, habitats) and (b) wilderness conservation is not only complementary but important for the long-term persistence of biodiversity. We develop two approaches to identify areas important for the conservation of biodiversity in terms of both wilderness quality and biodiversity representation, using Australia as a case study. We defined intact areas as sub-catchments with at least 70% or more vegetation that has not been subjected to extensive habitat loss and fragmentation as the result of land clearing. The first approach aims to achieve biodiversity representation goals in areas with intact native vegetation. The results of this approach would be extremely expensive to implement as they require a large portion of land. The second approach aims to achieve biodiversity representation goals anywhere across the landscape while placing a strong emphasis on identifying spatially compact intact areas. The results of this approach show the trade-offs between the economic costs of conservation and the size of conservation areas containing intact native vegetation. This manuscript provides a novel framework for identifying cost-effective biodiversity conservation priorities inclusive of wilderness quality.